W,
The point weights must be identical during the bare shaft and fletched comparisons. The object is to see how identical arrows form their different groupings ... although one of the groupings will be bare - and the other will be fletched.
For example, let's say you shoot 125 grain points on both the bare and fletched shafts.
During bare shaft tuning, the fletched arrow is considered "the truth" ... not the bare shaft. So all your comparisons of weak or stiff are based upon the fletched being "true" and the bare showing you what is needed to modify that "truth". The fletched arrows must be accurately centered on the target within your norm. The bare should be the variable that is used to modify the tuning. If your fletched arrows aren't hitting in a central place to begin with, either the shafts or your technique may be off enough to render bare shaft tuning impossible. Technique can give deceptive tuning patterns on the target, so do be aware of this.
Let's say the fletched are grouping in the middle, yet the bares are grouping to the right (assuming a RH archer). The fletching has corrected flight, yet the bare has not. Therefore, the observation on this example would be that the shafts are a bit weak (because the uncorrected bares have landed to the right of the fletched ones).
If using point weight only to make a correction, you would need to "stiffen" the dynamic spine of all the arrows in the test by reducing the point weight on all the arrows in the test ... say to 100 grains ... to make all shafts behave stiffer in flight. Then you would repeat the bare vs. fletched groupings several more times to see if the bares begin to group closer to the fletched. (You can do the same by shortening the lengths of all your shafts a very small amount if you don't want to change point weight.)
Let's say the bares now still group just a hair to the right and you want to nail it. Drop the point weight on all the arrows again ... say to 75 grains. Repeat the bare vs. fletched groupings. If the bare and fletched arrows are all now grouping in one spot, you have achieved your tuning. (You could do the same by shortening all the shafts another hair.)
You can also adjust the bow to achieve similar results by modifying the side plate offset (one of several possibilities). This is a fast, simple, and single step that can bring close groupings together without modifying the shafts.
If you read the link I provided with a very keen and slow eye ... many times ... and proceed exactly in the manner he describes, the mystery of it all will disappear and start to make absolute sense.
You may even wish to write down in your own hand the key steps to perform in the order that he advises as a handy reference absent the rest of the wording (or print it out and yellow-highlight the key steps).
You can often get the same fletched and bare shafts into one group using different point weights. However, this is not the bare shafting protocol. You want to get identically constructed shafts and point weights (with fletching only being the variable) to strike within the same group. This is how the fletched arrow becomes tuned to behave as perfectly as a bare shaft, with only the addition of fletching to help steer and forgive the existing perfection more accurately into the mark.
During the bare shafting processes, you should shoot all arrows in the same fashion, without "concentrating harder" or "really focusing" on the bare shaft shots you make. You want the "constant" of your technique present when shooting both the bares and fletched into the target, one after another within a single end, in order to get an accurate read on the groupings and what they mean.
And, as he mentions, you may find that you can't get the bares and fletched to tune, at which point you need to explore a different spine of shaft altogether.
You'll get it. It's a bit frustrating at first, yet if you absolutely nail his protocol to the letter, you'll quickly start observing the processes involved and be able to adjust your arrows more efficiently.
One rule of thumb that can prevent a lot of hair pulling: one can only bare shaft test as accurately as one can shoot. So, if during your regular shooting you are able to average a 20 yard group within, say, a one-foot circle, then you will use that as the size group you want the bare shafting processes to achieve. If you are within a two-foot circle at 20 yards, the bare shafting processes will be based on that size of a group. If you are within a six inch circle at 20 yards, then that smaller area will be what your bare shafting processes will be based upon.
Hang in there, and I hope some of this clarifies things a bit.